FEMS microbiology ecology最新文献_第6页

FEMSEC-thematic issue "Rhizosphere-a One Health concept". FEMSEC 专题 "根瘤菌圈--一个健康概念"。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-10-25 DOI: 10.1093/femsec/fiae136

Anton Hartmann, Luz de Bashan, Birgit Wassermann, Marcus A Horn, Angela Sessitsch

引用次数: 0

Habitat specificity modulates the bacterial biogeographic patterns in the Southern Ocean. 栖息地特异性改变了南大洋的细菌生物地理格局。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-10-25 DOI: 10.1093/femsec/fiae134

Mélanie Delleuze, Guillaume Schwob, Julieta Orlando, Karin Gerard, Thomas Saucède, Paul Brickle, Elie Poulin, Léa Cabrol

{"title":"Habitat specificity modulates the bacterial biogeographic patterns in the Southern Ocean.","authors":"Mélanie Delleuze, Guillaume Schwob, Julieta Orlando, Karin Gerard, Thomas Saucède, Paul Brickle, Elie Poulin, Léa Cabrol","doi":"10.1093/femsec/fiae134","DOIUrl":"10.1093/femsec/fiae134","url":null,"abstract":"Conceptual biogeographic frameworks have proposed that the relative contribution of environmental and geographical factors on microbial distribution depends on several characteristics of the habitat (e.g. environmental heterogeneity, species diversity, and proportion of specialist/generalist taxa), all of them defining the degree of habitat specificity, but few experimental demonstrations exist. Here, we aimed to determine the effect of habitat specificity on bacterial biogeographic patterns and assembly processes in benthic coastal ecosystems of the Southern Ocean (Patagonia, Falkland/Malvinas, Kerguelen, South Georgia, and King George Islands), using 16S rRNA gene metabarcoding. The gradient of habitat specificity resulted from a 'natural experimental design' provided by the Abatus sea urchin model, from the sediment (least specific habitat) to the intestinal tissue (most specific habitat). The phylogenetic composition of the bacterial communities showed a clear differentiation by site, driven by a similar contribution of geographic and environmental distances. However, the strength of this biogeographic pattern decreased with increasing habitat specificity: sediment communities showed stronger geographic and environmental divergence compared to gut tissue. The proportion of stochastic and deterministic processes contributing to bacterial assembly varied according to the geographic scale and the habitat specificity level. For instance, an increased contribution of dispersal limitation was observed in gut tissue habitat. Our results underscore the importance of considering different habitats with contrasting levels of specificity to better understand bacterial biogeography and assembly processes over oceanographic scales.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11523047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metabarcoding reveals ecologically distinct fungal assemblages in river and groundwater along an Austrian alpine to lowland gradient. 元条码揭示了奥地利从高山到低地梯度河流和地下水中生态独特的真菌群落。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-10-25 DOI: 10.1093/femsec/fiae139

Alice Retter, Christian Griebler, R Henrik Nilsson, Johannes Haas, Steffen Birk, Eva Breyer, Federico Baltar, Clemens Karwautz

{"title":"Metabarcoding reveals ecologically distinct fungal assemblages in river and groundwater along an Austrian alpine to lowland gradient.","authors":"Alice Retter, Christian Griebler, R Henrik Nilsson, Johannes Haas, Steffen Birk, Eva Breyer, Federico Baltar, Clemens Karwautz","doi":"10.1093/femsec/fiae139","DOIUrl":"10.1093/femsec/fiae139","url":null,"abstract":"Biodiversity, the source of origin, and ecological roles of fungi in groundwater are to this day a largely neglected field in fungal and freshwater ecology. We used DNA-based Illumina high-throughput sequence analysis of both fungal gene markers 5.8S and internal transcribed spacers region 2 (ITS2), improving taxonomic classification. This study focused on the groundwater and river mycobiome along an altitudinal and longitudinal transect of a pre-alpine valley in Austria in two seasons. Using Bayesian network modeling approaches, we identified patterns in fungal community assemblages that were mostly shaped by differences in landscape (climatic, topological, and geological) and environmental conditions. While river fungi were comparatively more diverse, unique fungal assemblages could be recovered from groundwater, including typical aquatic lineages such as Rozellomycota and Olpidiomycota. The most specious assemblages in groundwater were not linked to the input of organic material from the surface, and as such, seem to be sustained by characteristic groundwater conditions. Based on what is known from closely related fungi, our results suggest that the present fungal communities potentially contribute to mineral weathering, carbon cycling, and denitrification in groundwater. Furthermore, we were able to observe the effects of varying land cover due to agricultural practices on fungal biodiversity in groundwater ecosystems. This study contributes to improving our understanding of fungi in the subsurface aquatic biogeosphere.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11523079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Limited gut bacterial response of tuatara (Sphenodon punctatus) to dietary manipulation and captivity. 疣鼻天鹅（Sphenodon punctatus）肠道细菌对饮食控制和圈养的有限反应。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-10-25 DOI: 10.1093/femsec/fiae141

Carmen Hoffbeck, Danielle R M L Middleton, Susan N Keall, Chye-Mei Huang, An Pas, Kate Irving, Nicola J Nelson, Michael W Taylor

{"title":"Limited gut bacterial response of tuatara (Sphenodon punctatus) to dietary manipulation and captivity.","authors":"Carmen Hoffbeck, Danielle R M L Middleton, Susan N Keall, Chye-Mei Huang, An Pas, Kate Irving, Nicola J Nelson, Michael W Taylor","doi":"10.1093/femsec/fiae141","DOIUrl":"10.1093/femsec/fiae141","url":null,"abstract":"The bacteria of a host's digestive tract play crucial roles in digestion and pathogen resistance. Hosts living in captivity often have more human interaction and antibiotic use, in addition to differences in diet and environment, compared to their wild counterparts. Consequently, wild and captive animals frequently harbour different bacterial communities. We tested whether diversity of diet provided in captivity shifts the gut bacteria of tuatara, an endemic New Zealand reptile, at three captive sites, and examined how the gut community of these tuatara compares to those in the wild. Dietary manipulation did not cause a strong overall shift in tuatara gut bacteria, but individual tuatara did experience bacterial shifts during manipulation, which subsequently reverted after manipulation. We found that Bacteroides, a genus common in most vertebrate guts but rare in tuatara, increased significantly in the gut during manipulation, then decreased post-manipulation. Finally, the gut bacteria of captive tuatara significantly differed from those of wild tuatara, though most of the dominant bacterial genera found in wild tuatara persisted in captive tuatara. This work represents a first investigation of the captive tuatara bacterial community and establishes the sensitivity of the gut community to dietary manipulation and captivity for this relict reptile.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11523620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142461585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Widespread occurrence of dissolved oxygen anomalies, aerobic microbes, and oxygen-producing metabolic pathways in apparently anoxic environments. 在明显缺氧的环境中广泛存在溶解氧异常、好氧微生物和产氧代谢途径。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-10-25 DOI: 10.1093/femsec/fiae132

S Emil Ruff, Laura Schwab, Emeline Vidal, Jordon D Hemingway, Beate Kraft, Ranjani Murali

{"title":"Widespread occurrence of dissolved oxygen anomalies, aerobic microbes, and oxygen-producing metabolic pathways in apparently anoxic environments.","authors":"S Emil Ruff, Laura Schwab, Emeline Vidal, Jordon D Hemingway, Beate Kraft, Ranjani Murali","doi":"10.1093/femsec/fiae132","DOIUrl":"10.1093/femsec/fiae132","url":null,"abstract":"Nearly all molecular oxygen (O2) on Earth is produced via oxygenic photosynthesis by plants or photosynthetically active microorganisms. Light-independent O2 production, which occurs both abiotically, e.g. through water radiolysis, or biotically, e.g. through the dismutation of nitric oxide or chlorite, has been thought to be negligible to the Earth system. However, recent work indicates that O2 is produced and consumed in dark and apparently anoxic environments at a much larger scale than assumed. Studies have shown that isotopically light O2 can accumulate in old groundwaters, that strictly aerobic microorganisms are present in many apparently anoxic habitats, and that microbes and metabolisms that can produce O2 without light are widespread and abundant in diverse ecosystems. Analysis of published metagenomic data reveals that the enzyme putatively capable of nitric oxide dismutation forms four major phylogenetic clusters and occurs in at least 16 bacterial phyla, most notably the Bacteroidota. Similarly, a re-analysis of published isotopic signatures of dissolved O2 in groundwater suggests in situ production in up to half of the studied environments. Geochemical and microbiological data support the conclusion that \"dark oxygen production\" is an important and widespread yet overlooked process in apparently anoxic environments with far-reaching implications for subsurface biogeochemistry and ecology.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbial solutions must be deployed against climate catastrophe. 必须采用微生物解决方案来应对气候灾难。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-10-25 DOI: 10.1093/femsec/fiae144

Raquel Peixoto, Christian R Voolstra, Lisa Y Stein, Philip Hugenholtz, Joana Falcao Salles, Shady A Amin, Max Häggblom, Ann Gregory, Thulani P Makhalanyane, Fengping Wang, Nadège Adoukè Agbodjato, Yinzhao Wang, Nianzhi Jiao, Jay T Lennon, Antonio Ventosa, Patrik M Bavoil, Virginia Miller, Jack A Gilbert

引用次数: 0

Can longer lifespan be associated with gut microbiota involvement in lipid metabolism? 寿命的延长是否与肠道微生物群参与脂质代谢有关？

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-10-25 DOI: 10.1093/femsec/fiae135

Sára Šardzíková, Marta Gajewska, Norbert Gałka, Matúš Štefánek, Andrej Baláž, Martina Garaiová, Roman Holič, Wiesław Świderek, Katarína Šoltys

{"title":"Can longer lifespan be associated with gut microbiota involvement in lipid metabolism?","authors":"Sára Šardzíková, Marta Gajewska, Norbert Gałka, Matúš Štefánek, Andrej Baláž, Martina Garaiová, Roman Holič, Wiesław Świderek, Katarína Šoltys","doi":"10.1093/femsec/fiae135","DOIUrl":"10.1093/femsec/fiae135","url":null,"abstract":"Biological aging is linked to altered body composition and reduced neuroactive steroid hormones like dehydroepiandrosterone sulfate (DHEAS), which can stimulate the GABA signaling pathway via gut microbiota. Our study examined the association of gut microbiota with lifespan in mice through comprehensive analysis of its composition and functional involvement in cholesterol sulfate, a precursor of DHEAS, metabolism. We used 16S rRNA and metagenomic sequencing, followed by metabolic pathway prediction and thin layer chromatography and MALDI-TOF cholesterol sulfate identification. Significant increases in bacteria such as Bacteroides, typical for long-lived and Odoribacter and Colidextribacter, specific for short-lived mice were detected. Furthermore, for males (Rikenella and Alloprevotella) and females (Lactobacillus and Bacteroides), specific bacterial groups emerged as predictors (AUC = 1), highlighting sex-specific patterns. Long-lived mice showed a strong correlation of Bacteroides (0.918) with lipid and steroid hormone metabolism, while a negative correlation of GABAergic synapse with body weight (-0.589). We found that several Bacteroides species harboring the sulfotransferase gene and gene cluster for sulfonate donor synthesis are involved in converting cholesterol to cholesterol sulfate, significantly higher in the feces of long-lived individuals. Overall, we suggest that increased involvement of gut bacteria, mainly Bacteroides spp., in cholesterol sulfate synthesis could ameliorate aging through lipid metabolism.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11503954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142362686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Pseudogymnoascus destructans invasion stage impacts the skin microbial functions of highly vulnerable Myotis lucifugus. 破坏性假丝酵母菌的入侵阶段会影响高度脆弱的滇金丝猴的皮肤微生物功能。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-10-25 DOI: 10.1093/femsec/fiae138

Virginie Lemieux-Labonté, Jananan S Pathmanathan, Yves Terrat, Nicolas Tromas, Anouk Simard, Catherine G Haase, Cori L Lausen, Craig K R Willis, François-Joseph Lapointe

{"title":"Pseudogymnoascus destructans invasion stage impacts the skin microbial functions of highly vulnerable Myotis lucifugus.","authors":"Virginie Lemieux-Labonté, Jananan S Pathmanathan, Yves Terrat, Nicolas Tromas, Anouk Simard, Catherine G Haase, Cori L Lausen, Craig K R Willis, François-Joseph Lapointe","doi":"10.1093/femsec/fiae138","DOIUrl":"10.1093/femsec/fiae138","url":null,"abstract":"The role of the skin microbiome in resistance and susceptibility of wildlife to fungal pathogens has been examined from a taxonomic perspective but skin microbial function, in the context of fungal infection, has yet to be studied. Our objective was to understand effects of a bat fungal pathogen site infection status and course of invasion on skin microbial function. We sampled seven hibernating colonies of Myotis lucifugus covering three-time points over the course of Pseudogymnoascus destructans (Pd) invasion and white nose syndrome (pre-invasion, epidemic, and established). Our results support three new hypotheses about Pd and skin functional microbiome: (1) there is an important effect of Pd invasion stage, especially at the epidemic stage; (2) disruption by the fungus at the epidemic stage could decrease anti-fungal functions with potential negative effects on the microbiome and bat health; (3) the collection site might have a larger influence on microbiomes at the pre-invasion stage rather than at epidemic and established stages. Future studies with larger sample sizes and using meta-omics approaches will help confirm these hypotheses, and determine the influence of the microbiome on wildlife survival to fungal disease.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11523048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142461586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Organic farming systems improve soil quality and shape microbial communities across a cotton-based crop rotation in an Indian Vertisol 有机耕作制度改善了印度椎体土壤质量，并塑造了棉花轮作中的微生物群落

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-09-18 DOI: 10.1093/femsec/fiae127

Martina Lori, Dominika Kundel, Paul Mäder, Akanksha Singh, Dharmendra Patel, Bhupendra Singh Sisodia, Amritbir Riar, Hans-Martin Krause

{"title":"Organic farming systems improve soil quality and shape microbial communities across a cotton-based crop rotation in an Indian Vertisol","authors":"Martina Lori, Dominika Kundel, Paul Mäder, Akanksha Singh, Dharmendra Patel, Bhupendra Singh Sisodia, Amritbir Riar, Hans-Martin Krause","doi":"10.1093/femsec/fiae127","DOIUrl":"https://doi.org/10.1093/femsec/fiae127","url":null,"abstract":"The adverse effects of intensified cropland practices on soil quality and biodiversity become especially evident in India, where nearly 60% of land is dedicated to cultivation, and almost 30% of soil is already degraded. Intensive agricultural practice significantly contributes to soil degradation, highlighting the crucial need for effective countermeasures to support sustainable development goals. A long-term experiment, established in the semi-arid Nimar Valley (India) in 2007, monitors the effect of organic and conventional management on the plant-soil system in a Vertisol. The focus of our study was to assess how organic and conventional farming systems affect biological and chemical soil quality indicators. Additionally, we followed the community structure of the soil microbiome throughout the vegetation phase under soya or cotton cultivation in the year 2019. We found that organic farming enhanced soil organic carbon and nitrogen content, increased microbial abundance and activity, and fostered distinct microbial communities associated with traits in nutrient mineralization. In contrast, conventional farming enhanced the abundance of bacteria involved in ammonium oxidation suggesting high nitrification and subsequent nitrogen losses with regular mineral fertilization. Our findings underscore the value of adopting organic farming approaches in semi-arid subtropical regions to rectify soil quality and minimize nitrogen losses.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"75 1","pages":""},"PeriodicalIF":4.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142254392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Geothermal ecosystems on Mt. Erebus, Antarctica, support diverse and taxonomically novel biota 南极洲埃里伯斯山的地热生态系统支持着多种多样、分类新颖的生物群落

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-09-18 DOI: 10.1093/femsec/fiae128

Trine Bertram Rasmussen, Stephen E Noell, Craig W Herbold, Ian A Dickie, Roanna Richards-Babbage, Matthew B Stott, S Craig Cary, Ian R McDonald

{"title":"Geothermal ecosystems on Mt. Erebus, Antarctica, support diverse and taxonomically novel biota","authors":"Trine Bertram Rasmussen, Stephen E Noell, Craig W Herbold, Ian A Dickie, Roanna Richards-Babbage, Matthew B Stott, S Craig Cary, Ian R McDonald","doi":"10.1093/femsec/fiae128","DOIUrl":"https://doi.org/10.1093/femsec/fiae128","url":null,"abstract":"Mt. Erebus, Antarctica, is the southernmost active volcano in the world and harbors diverse geothermally unique ecosystems, including ‘Subglacial’ and ‘Exposed’ features, surrounded by a vast desert of ice and snow. Previous studies, while limited in scope, have highlighted the unique and potentially endemic biota of Mt. Erebus. Here, we provide an amplicon-based biodiversity study across all domains of life and all types of geothermal features, with physicochemical and biological data from 48 samples (39 Exposed and 9 Subglacial) collected through various field seasons. We found potentially high taxonomic novelty among prokaryotes and fungi, supporting past hypotheses of high endemism due to the distinctive and isolated environment; in particular, the large number of taxonomically divergent fungal sequences was surprising. We found that different site types had unique physicochemistry and biota; Exposed sites were warmer than Subglacial (median: 40 vs 10°C for Exposed and Subglacial, respectively) and tended to have more photosynthetic organisms (Cyanobacteria and Chlorophyta). Subglacial sites had more Actinobacteriota, correlated with greater concentrations of Ca and Mg present. Our results also suggest potential human impacts on these remote, highly significant sites, finding evidence for fungal taxa normally associated with wood decay. In this study, we provide a blueprint for future work aimed at better understanding the novel biota of Mt. Erebus.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"187 1","pages":""},"PeriodicalIF":4.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142254442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0